ordihull {vegan} | R Documentation |
Functions to add convex hulls, arrows, line segments, regular grids of
points, `spider' graphs, ellipses or cluster dendrogram
to ordination diagrams. The
ordination diagrams can be produced by vegan
plot.cca
, plot.decorana
or
ordiplot
.
ordihull(ord, groups, display = "sites", draw = c("lines","polygon"), show.groups, ...) ordiarrows(ord, groups, levels, replicates, display = "sites", show.groups, startmark, ...) ordisegments(ord, groups, levels, replicates, display = "sites", show.groups, ...) ordigrid(ord, levels, replicates, display = "sites", ...) ordispider(ord, groups, display="sites", w = weights(ord, display), show.groups, ...) ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf, draw = c("lines","polygon"), w = weights(ord, display), show.groups, ...) ordicluster(ord, cluster, prune = 0, display = "sites", w = weights(ord, display), ...)
ord |
An ordination object or an ordiplot object. |
groups |
Factor giving the groups for which the graphical item is drawn. |
levels, replicates |
Alternatively, regular
groups can be defined with arguments levels and
replicates , where levels gives the number of groups,
and replicates the number of successive items at the same
group. |
display |
Item to displayed. |
draw |
Use either lines or polygon to
draw the
line. Graphical parameters are passed to both. The main difference
is that polygon s may be filled and non-transparent. |
show.groups |
Show only given groups. This can be a vector, or
TRUE if you want to show items for which condition is
TRUE . This argument makes it possible to use different
colours and line types for groups. The default is to show all
groups. |
startmark |
plotting characer used to mark the first
item. The default is to use no mark, and for instance,
startmark = 1 will draw a circle. For other plotting characters,
see pch in points . |
w |
Weights used to find the average within group. Weights are
used automatically for cca
and decorana results, unless undone by the
user. w=NULL sets equal weights to all points. |
kind |
Whether standard deviations of points (sd ) or
standard deviations of their (weighted) averages (se ) are
used. |
conf |
Confidence limit for ellipses, e.g. 0.95. If given, the
corresponding sd or se is multiplied with the
corresponding value found from the Chi-squared distribution with
2df. |
cluster |
Result of hierarchic cluster analysis, such as
hclust or agnes . |
prune |
Number of upper level hierarchies removed from the
dendrogram. If prune >0, dendrogram will be
disconnected. |
... |
Parameters passed to graphical functions such
as lines , segments ,
arrows , polygon or to
scores to select axes and
scaling etc. |
Function ordihull
draws lines
or
polygon
s for the convex
hulls found by function chull
encircling
the items in the groups.
Function ordiarrows
draws
arrows
and ordisegments
draws line
segments
between successive items in the
groups. Function ordigrid
draws line
segments
both within the groups and for the
corresponding items among the groups.
Function ordispider
draws a `spider' diagram where each point
is connected to the group centroid with
segments
. Weighted centroids are used in the
correspondence analysis methods cca
and
decorana
or if the user gives the weights in the
call. If ordispider
is called with cca
or
rda
result without groups
argument, the function
connects each `WA' scores to the correspoding `LC' score.
Function ordiellipse
draws lines
or
polygon
s for dispersion
ellipse
using either standard deviation of
point scores or standard error of the (weighted) average of
scores, and the (weighted) correlation defines the direction of the
principal axis of the ellipse. The function requires package
ellipse. An ellipsoid hull can be drawn with function
ellipsoidhull
of package cluster.
Function ordicluster
overlays a cluster dendrogram onto
ordination. It needs the result from a hierarchic clustering such as
hclust
or agnes
, or other
with a similar structure. Function ordicluster
connects
cluster centroids to each other with line
segments
. Function uses centroids of all points in the
clusters, and is therefore similar to average linkage methods.
These functions add graphical items to ordination graph: You must draw a graph first.
Jari Oksanen
The functions pass parameters to basic graphical functions, and
you may wish to change the default values in arrows
,
lines
, segments
and
polygon
. You can pass
parameters to scores
as well. Other underlying functions
are chull
and ellipse
.
data(dune) data(dune.env) mod <- cca(dune ~ Moisture, dune.env) attach(dune.env) ## pass non-graphical arguments without warnings plot(mod, type="n", scaling = 3) ordihull(mod, Moisture, scaling = 3) ordispider(mod, col="red", scaling = 3) plot(mod, type = "p", display="sites") ordicluster(mod, hclust(vegdist(dune)), prune=3, col = "blue") # The following is not executed automatically because it needs # a non-standard library `ellipse'. ## Not run: ordiellipse(mod, Moisture, kind="se", conf=0.95, lwd=2, col="blue") ## End(Not run)